Saltational episodes of reticulate evolution in the Drosophila saltans species group

Phylogenomics revealed reticulate evolution to be widespread across taxa, but whether reticulation is due to low statistical power (soft polytomy) or it is a true evolutionary pattern (hard polytomy) remains a field of investigation. Here, we investigate the phylogeny and quantify reticulation in the Drosophila saltans species group, a Neotropical clade of the subgenus Sophophora comprising 23 species arranged in five subgroups, namely cordata , elliptica , parasaltans , saltans and sturtevanti . The relationships within and between the subgroups have long been problematic. We sequenced and assembled the genomes of 15 species. Phylogenetic analyses revealed conflicting topologies between the X chromosome, autosomes and the mitochondria. We extended the ABBA-BABA test of asymmetry in phylogenetic discordance to cases where no "true" species tree could be inferred, and applied our new test (called 2A2B) to ≥50 kb-long 1,797 syntenic blocks with conserved collinearity across Neotropical Sophophora. High incidences of reticulation (sometimes up to 90% of the blocks) were restricted to three nodes on the tree, at the split between the cordata-elliptica-saltans subgroups and at the origin of the sturtevanti and saltans subgroups. By contrast, cases with asymmetric discordances, which are often interpreted as evidence for interspecific introgression, did not exceed ~7% of the blocks. Historical biogeography analysis revealed that short inter-speciation times and greater overlap of ancestral geographical ranges can explain cases with predominant reticulation. Therefore, episodic rapid radiations have played a major role in the evolution of this largely understudied Neotropical clade. ### Competing Interest Statement The authors have declared no competing interest.